I acknowledge your efforts in outlining and expressing your concerns, @Operations_Monkey. I also certainly understand the convenience of rectifying this concern to keep you from deleting the duplicate payments reflected in your QuickBooks Desktop (QBDT) Company.

Since the Community is a public forum, we’re unable to proceed in accessing your account to determine an appropriate resolution. Moreover, our phone support has the tools to trigger an investigation concerning the aforementioned concerns.

In this manner, I’d recommend contacting our Technical Support Team to double-check what causing your payments to be duplicated and the unspecified reason for creating another Undeposited Funds account. 

I understand that you have already contacted them to get everything sorted out. However, the best option we have here is to contact them to initiate a thorough examination of your account.

Here’s how:

1. From your QuickBooks Desktop account, click the Help menu at the top.
2. Click the QuickBooks Desktop Help menu and select Contact Us.
3. Provide some information about this concern in the search box, then select Continue.
4. Sign in to your Intuit account and tap Continue. Afterward, select Continue with my account.
5. Please enter the code that will be sent to you via email and select Continue.
6. From there, select how you want to connect with us. It’s either to chat with us or Have us call you.

Here’s an article you can check out for other ways of contacting them. Support hours and schedules are also outlined in this resource: Contact QuickBooks Desktop support.

I’ll be around the corner if you need an extra pair of hands in any QuickBooks-related matters. Stay safe!